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11. Confronting Racism in Chemistry Journals

Author

Burrows, Cynthia J, Huang, Jiaxiang, Wang, Shu, Kim, Hyun Jae, Meyer, Gerald J, Schanze, Kirk, Lee, T Randall, Lutkenhaus, Jodie L, Kaplan, David, Jones, Christopher, Bertozzi, Carolyn, Kiessling, Laura, Mulcahy, Mary Beth, Lindsley, Craig W, Finn, MG, Blum, Joel D, Kamat, Prashant, Choi, Wonyong, Snyder, Shane, Aldrich, Courtney C, Rowan, Stuart, Liu, Bin, Liotta, Dennis, Weiss, Paul S, Zhang, Deqing, Ganesh, Krishna N, Atwater, Harry A, Gooding, J Justin, Allen, David T, Voigt, Christopher A, Sweedler, Jonathan, Schepartz, Alanna, Rotello, Vincent, Lecommandoux, Sébastien, Sturla, Shana J, Hammes-Schiffer, Sharon, Buriak, Jillian, Steed, Jonathan W, Wu, Hongwei, Zimmerman, Julie, Brooks, Bryan, Savage, Phillip, Tolman, William, Hofmann, Thomas F, Brennecke, Joan F, Holme, Thomas A, Merz, Kenneth M, Scuseria, Gustavo, Jorgensen, William, Georg, Gunda I, Wang, Shaomeng, Proteau, Philip, Yates, John R, Stang, Peter, Walker, Gilbert C, Hillmyer, Marc, Taylor, Lynne S, Odom, Teri W, Carreira, Erick, Rossen, Kai, Chirik, Paul, Miller, Scott J, Shea, Joan-Emma, McCoy, Anne, Zanni, Martin, Hartland, Gregory, Scholes, Gregory, Loo, Joseph A, Milne, James, Tegen, Sarah B, Kulp, Daniel T, and Laskin, Julia

Subjects
Chemical Sciences
Published
2020

12. Update to Our Reader, Reviewer, and Author CommunitiesApril 2020

Author

Burrows, Cynthia J, Wang, Shu, Kim, Hyun Jae, Meyer, Gerald J, Schanze, Kirk, Lee, T Randall, Lutkenhaus, Jodie L, Kaplan, David, Jones, Christopher, Bertozzi, Carolyn, Kiessling, Laura, Mulcahy, Mary Beth, Lindsley, Craig W, Finn, MG, Blum, Joel D, Kamat, Prashant, Aldrich, Courtney C, Rowan, Stuart, Liu, Bin, Liotta, Dennis, Weiss, Paul S, Zhang, Deqing, Ganesh, Krishna N, Sexton, Patrick, Atwater, Harry A, Gooding, J Justin, Allen, David T, Voigt, Christopher A, Sweedler, Jonathan, Schepartz, Alanna, Rotello, Vincent, Lecommandoux, Sébastien, Sturla, Shana J, Hammes-Schiffer, Sharon, Buriak, Jillian, Steed, Jonathan W, Wu, Hongwei, Zimmerman, Julie, Brooks, Bryan, Savage, Phillip, Tolman, William, Hofmann, Thomas F, Brennecke, Joan F, Holme, Thomas A, Merz, Kenneth M, Scuseria, Gustavo, Jorgensen, William, Georg, Gunda I, Wang, Shaomeng, Proteau, Philip, Yates, John R, Stang, Peter, Walker, Gilbert C, Hillmyer, Marc, Taylor, Lynne S, Odom, Teri W, Carreira, Erick, Rossen, Kai, Chirik, Paul, Miller, Scott J, McCoy, Anne, Shea, Joan-Emma, Zanni, Martin, Murphy, Catherine, Scholes, Gregory, and Loo, Joseph A

Subjects
Chemical Sciences
Published
2020

13. Update to Our Reader, Reviewer, and Author Communities-April 2020.

Author

Burrows, Cynthia J, Wang, Shu, Kim, Hyun Jae, Meyer, Gerald J, Schanze, Kirk, Lee, T Randall, Lutkenhaus, Jodie L, Kaplan, David, Jones, Christopher, Bertozzi, Carolyn, Kiessling, Laura, Mulcahy, Mary Beth, Lindsley, Craig W, Finn, MG, Blum, Joel D, Kamat, Prashant, Aldrich, Courtney C, Rowan, Stuart, Bin Liu, Liotta, Dennis, Weiss, Paul S, Zhang, Deqing, Ganesh, Krishna N, Sexton, Patrick, Atwater, Harry A, Gooding, J Justin, Allen, David T, Voigt, Christopher A, Sweedler, Jonathan, Schepartz, Alanna, Rotello, Vincent, Lecommandoux, Sébastien, Sturla, Shana J, Hammes-Schiffer, Sharon, Buriak, Jillian, Steed, Jonathan W, Wu, Hongwei, Zimmerman, Julie, Brooks, Bryan, Savage, Phillip, Tolman, William, Hofmann, Thomas F, Brennecke, Joan F, Holme, Thomas A, Merz, Kenneth M, Scuseria, Gustavo, Jorgensen, William, Georg, Gunda I, Wang, Shaomeng, Proteau, Philip, Yates, John R, Stang, Peter, Walker, Gilbert C, Hillmyer, Marc, Taylor, Lynne S, Odom, Teri W, Carreira, Erick, Rossen, Kai, Chirik, Paul, Miller, Scott J, McCoy, Anne, Shea, Joan-Emma, Zanni, Martin, Murphy, Catherine, Scholes, Gregory, and Loo, Joseph A

Subjects
Chemical Sciences, General Chemistry
Published
2020

14. Engineered plant control of associative nitrogen fixation

Author

Haskett, Timothy L., Paramasivan, Ponraj, Mendes, Marta D., Green, Patrick, Geddes, Barney A., Knights, Hayley E., Jorrin, Beatriz, Ryu, Min-Hyung, Brett, Paul, Voigt, Christopher A., Oldroyd, Giles E. D., and Poole, Philip S.

Published
2022

16. Infrared‐Scattering by Programmable Peptide‐Melanin Microparticles.

Author

Lee, Di Sheng, Yuan, Weize, and Voigt, Christopher A.

Subjects
STRUCTURAL colors, OPTICAL materials, SYNTHETIC biology, MOLECULAR dynamics, PHENOL oxidase, BIOPOLYMERS
Abstract

Natural melanin polymers, biosynthesized from free tyrosine, assemble into microstructures that interact with light, producing a wide range of photonic properties. These structures are formed by mechanisms that are difficult to control to create new optical materials. Here, simple pentapeptides YXXXY is presented, where the XXX controls self‐assembly into microstructures, after which the Y's are polymerized by tyrosinase into melanin. It sought to computationally predict peptides that will assemble into two‐layer films that exhibit structural color and infrared (IR) scattering. Three peptides (YPIIY, YLPIY, YVPAY) are synthesized and found to form a two‐layer film exhibiting structural color. YLPIY‐melanin also forms a stable coating with scattering peaks in the near‐ and mid‐IR. This coating reduces the signature of a hotplate (37 °C) as seen by a thermal camera. This synthetic peptidic material is the first to exhibit IR‐scattering, opening the possibility of incorporating this function into bio‐compatible fibers, textiles, and plastics. [ABSTRACT FROM AUTHOR]

Published
2024
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23. Primary Human Colonic Mucosal Barrier Crosstalk with Super Oxygen-Sensitive Faecalibacterium prausnitzii in Continuous Culture

Author

Zhang, Jianbo, Huang, Yu-Ja, Yoon, Jun Young, Kemmitt, John, Wright, Charles, Schneider, Kirsten, Sphabmixay, Pierre, Hernandez-Gordillo, Victor, Holcomb, Steven J., Bhushan, Brij, Rohatgi, Gar, Benton, Kyle, Carpenter, David, Kester, Jemila C., Eng, George, Breault, David T., Yilmaz, Omer, Taketani, Mao, Voigt, Christopher A., Carrier, Rebecca L., Trumper, David L., and Griffith, Linda G.

Published
2021
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28. Discovery of Reactive Microbiota-Derived Metabolites that Inhibit Host Proteases.

Author

Guo, Chun-Jun, Chang, Fang-Yuan, Wyche, Thomas P, Backus, Keriann M, Acker, Timothy M, Funabashi, Masanori, Taketani, Mao, Donia, Mohamed S, Nayfach, Stephen, Pollard, Katherine S, Craik, Charles S, Cravatt, Benjamin F, Clardy, Jon, Voigt, Christopher A, and Fischbach, Michael A

Subjects
Feces, Animals, Humans, Bacteria, Bacillus subtilis, Escherichia coli, Pyrazines, Peptide Synthases, Phylogeny, Microbiota, Gastrointestinal Microbiome, biosynthetic gene cluster, metagenomics, microbiome, natural products, peptide aldehyde, protease inhibitor, synthetic biology, Developmental Biology, Biological Sciences, Medical and Health Sciences
Abstract

The gut microbiota modulate host biology in numerous ways, but little is known about the molecular mediators of these interactions. Previously, we found a widely distributed family of nonribosomal peptide synthetase gene clusters in gut bacteria. Here, by expressing a subset of these clusters in Escherichia coli or Bacillus subtilis, we show that they encode pyrazinones and dihydropyrazinones. At least one of the 47 clusters is present in 88% of the National Institutes of Health Human Microbiome Project (NIH HMP) stool samples, and they are transcribed under conditions of host colonization. We present evidence that the active form of these molecules is the initially released peptide aldehyde, which bears potent protease inhibitory activity and selectively targets a subset of cathepsins in human cell proteomes. Our findings show that an approach combining bioinformatics, synthetic biology, and heterologous gene cluster expression can rapidly expand our knowledge of the metabolic potential of the microbiota while avoiding the challenges of cultivating fastidious commensals.

Published
2017

39. EvoAI enables extreme compression and reconstruction of the protein sequence space

Author

Zhang, Shuyi, primary, Ma, Ziyuan, additional, Li, Wenjie, additional, Shen, Yunhao, additional, Xu, Yunxin, additional, Liu, Gengjiang, additional, Chang, Jiamin, additional, Li, Zeju, additional, Qin, Hong, additional, Tian, Boxue, additional, Gong, Haipeng, additional, Liu, David, additional, Thuronyi, B, additional, and Voigt, Christopher, additional

Published
2024
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44. Synthetic biology open language visual (SBOL Visual) version 2.3

Author

Baig Hasan, Fontanarossa Pedro, Kulkarni Vishwesh, McLaughlin James, Vaidyanathan Prashant, Bartley Bryan, Bhakta Shyam, Bhatia Swapnil, Bissell Mike, Clancy Kevin, Cox Robert Sidney, Goñi Moreno Angel, Gorochowski Thomas, Grunberg Raik, Lee Jihwan, Luna Augustin, Madsen Curtis, Misirli Goksel, Nguyen Tramy, Le Novere Nicolas, Palchick Zachary, Pocock Matthew, Roehner Nicholas, Sauro Herbert, Scott-Brown James, Sexton John T., Stan Guy-Bart, Tabor Jeffrey J., Terry Logan, Vazquez Vilar Marta, Voigt Christopher A., Wipat Anil, Zong David, Zundel Zach, Beal Jacob, and Myers Chris

Subjects
diagrams, sbol visual, standards, Biotechnology, TP248.13-248.65
Abstract

People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. The Synthetic Biology Open Language Visual (SBOL Visual) has been developed as a standard for organizing and systematizing such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. This document details version 2.3 of SBOL Visual, which builds on the prior SBOL Visual 2.2 in several ways. First, the specification now includes higher-level “interactions with interactions,” such as an inducer molecule stimulating a repression interaction. Second, binding with a nucleic acid backbone can be shown by overlapping glyphs, as with other molecular complexes. Finally, a new “unspecified interaction” glyph is added for visualizing interactions whose nature is unknown, the “insulator” glyph is deprecated in favor of a new “inert DNA spacer” glyph, and the polypeptide region glyph is recommended for showing 2A sequences.

Published
2021
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46. Engineering orthogonal signalling pathways reveals the sparse occupancy of sequence space

Author

McClune, Conor J., Alvarez-Buylla, Aurora, Voigt, Christopher A., and Laub, Michael T.

Subjects
Physiological aspects, Genetic aspects, Methods, Protein engineering -- Methods, Cellular signal transduction -- Genetic aspects, Signaling peptides and proteins -- Physiological aspects -- Genetic aspects
Abstract

Author(s): Conor J. McClune [sup.1] [sup.2] , Aurora Alvarez-Buylla [sup.1] , Christopher A. Voigt [sup.2] , Michael T. Laub [sup.1] [sup.3] Author Affiliations: (1) Department of Biology, Massachusetts Institute of [...], Gene duplication is a common and powerful mechanism by which cells create new signalling pathways.sup.1,2, but recently duplicated proteins typically must become insulated from each other and from other paralogues to prevent unwanted crosstalk.sup.3. A similar challenge arises when new sensors or synthetic signalling pathways are engineered within cells or transferred between genomes. How easily new pathways can be introduced into cells depends on the density and distribution of paralogous pathways in the sequence space that is defined by their specificity-determining residues.sup.4,5. Here we directly investigate how crowded this sequence space is, by generating novel two-component signalling proteins in Escherichia coli using cell sorting coupled to deep sequencing to analyse large libraries designed on the basis of coevolutionary patterns. We produce 58 insulated pathways comprising functional kinase-substrate pairs that have different specificities than their parent proteins, and demonstrate that several of these new pairs are orthogonal to all 27 paralogous pathways in E. coli. Additionally, from the kinase-substrate pairs generated, we identify sets consisting of six pairs that are mutually orthogonal to each other, which considerably increases the two-component signalling capacity of E. coli. These results indicate that sequence space is not densely occupied. The relative sparsity of paralogues in sequence space suggests that new insulated pathways can arise easily during evolution, or be designed de novo. We demonstrate the latter by engineering a signalling pathway in E. coli that responds to a plant cytokinin, without crosstalk to extant pathways. Our work also demonstrates how coevolution-guided mutagenesis and the mapping of sequence space can be used to design large sets of orthogonal protein-protein interactions. Engineered two-component signalling proteins in Escherichia coli have residue specificities different to their parent proteins and are orthogonal to all extant paralogues, demonstrating that sequence space is not densely occupied.

Published
2019
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49. Genetic Sensor for Strong Methylating Compounds

Author

Moser, Felix, Horwitz, Andrew, Chen, Jacinto, Lim, Wendell A, and Voigt, Christopher A

Subjects
Biochemistry and Cell Biology, Biological Sciences, Genetics, Biosensing Techniques, DNA Methylation, Escherichia coli, Promoter Regions, Genetic, Saccharomyces cerevisiae, synthetic biology, genetic circuit, genetic device, fumigant, Gal4, Medicinal and Biomolecular Chemistry, Biomedical Engineering, Biochemistry and cell biology, Bioinformatics and computational biology
Abstract

Methylating chemicals are common in industry and agriculture and are often toxic, partly due to their propensity to methylate DNA. The Escherichia coli Ada protein detects methylating compounds by sensing aberrant methyl adducts on the phosphoester backbone of DNA. We characterize this system as a genetic sensor and engineer it to lower the detection threshold. By overexpressing Ada from a plasmid, we improve the sensor’s dynamic range to 350-fold induction and lower its detection threshold to 40 μM for methyl iodide. In eukaryotes, there is no known sensor of methyl adducts on the phosphoester backbone of DNA. By fusing the N-terminal domain of Ada to the Gal4 transcriptional activation domain, we built a functional sensor for methyl phosphotriester adducts in Saccharomyces cerevisiae. This sensor can be tuned to variable specifications by altering the expression level of the chimeric sensor and changing the number of Ada operators upstream of the Gal4-sensitive reporter promoter. These changes result in a detection threshold of 28 μM and 5.2-fold induction in response to methyl iodide. When the yeast sensor is exposed to different SN1 and SN2 alkylating compounds, its response profile is similar to that observed for the native Ada protein in E. coli, indicating that its native function is retained in yeast. Finally, we demonstrate that the specifications achieved for the yeast sensor are suitable for detecting methylating compounds at relevant concentrations in environmental samples. This work demonstrates the movement of a sensor from a prokaryotic to eukaryotic system and its rational tuning to achieve desired specifications.

Published
2013

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